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DOE OSTI2026

Self-Admitted Technical Debt in Scientific Software: Prioritization, Sentiment, and Propagation Across Artifacts

Self-admitted technical debt (SATD) impairs scientific software (SSW), yet its prioritization, sentiment, persistence, and propagation remains underexplored. Understanding how SSW developers express, and address SATD is crucial for improving SSW maintenance, and tooling. This study investigates how SATD types and artifacts in SSW are prioritized, how sentiment relates to urgency, SATD removal and resolution rates, and the extent to which SATD propagates across artifacts. We analyzed nine SSW repositories using a SATD classification model and a semantic embedding-based prioritization heuristic. SATD was examined across multiple artifacts, with sentiment assessed via a fine-tuned transformer. Propagation was traced, priority scores compared to static analysis, and removal and resolution rates quantified. SATD in comments, commits, and pull requests receive higher priority than SATD in issues, with negative sentiment amplifying urgency. Resolution and removal rates lag behind open-source software (OSS) averages. Most SATD remains confined to the originating artifact, but longer propagation chains are rare and correlate with higher priority, highlighting persistent and high impact debt. Prioritization is influenced by artifact type and sentiment, while low removal and resolution rates signal persistent debt. Cross-artifact propagation marks high priority, unresolved SATD, providing empirical guidance for targeted monitoring, review prioritization, and tool supported maintenance in SSW.

Melin, Eric [Boise State University]↗

DOE OSTI2022

pnnl/hydraconda

A framework for developing scientific computing codes for projects was developed that accommodates both explorations as well as, simultaneously, software engineering rigor. This is accomplished by organizing modular yet composable and related computational environments. Also known as Management of Multiple Computational Environments

alDosari, Majid↗

NASA NTRS2009

Refactoring and Componentizing Legacy Codes: GMI Case Study

As Earth science applications grow increasingly complex over time, maintenance of such software becomes a significant challenge. In general, the software subsystems were designed, implemented and integrated (over an extended period of time) by different groups that did not follow the same software design standard. The objective was understandably to obtain scientific results quickly, but this goal was often achieved at the expense of good software practices. With that pattern of development, the cost of incremental changes to the applications grow ominously large. This increase in effort, tends to squeeze development resources and largely prevent any systematic attempt to reintroduce better software practices and thereby enhance the maintainability of the software. In this paper, we present the process we used to incrementally refactor and componentize the Global Modeling Initiative code to make it more understandable, maintainable, flexible and extensible. The resulting product not only preserves the scientific integrity of the original code but also extends the capabilities of the code for several applications.

Kouatchou, Jules↗

NASA NTRS2004

NASA's Swarm Missions: The Challenge of Building Autonomous Software

The days of watching a massive manned cylinder thrust spectacularly off a platform into space might rapidly become ancient history when the National Aeronautics and Space Administration (NASA) introduces its new millenium mission class. Motivated by the need to gather more data than is possible with a single spacecraft, scientists have developed a new class of missions based on the efficiency and cooperative nature of a hive culture. The missions, aptly dubbed nanoswarm will be little more than mechanized colonies cooperating in their exploration of the solar system. Each swarm mission can have hundreds or even thousands of cooperating intelligent spacecraft that work in teams. The spacecraft must operate independently for long periods both in teams and individually, as well as have autonomic properties - self-healing, -configuring, -optimizing, and -protecting- to survive the harsh space environment. One swarm mission under concept development for 2020 to 2030 is the Autonomous Nano Technology Swarm (ANTS), in which a thousand picospacecraft, each weighing less than three pounds, will work cooperatively to explore the asteroid belt. Some spacecraft will form teams to catalog asteroid properties, such as mass, density, morphology, and chemical composition, using their respective miniature scientific instruments. Others will communicate with the data gatherers and send updates to mission elements on Earth. For software and systems development, this is uncharted territory that calls for revolutionary techniques.

Truszkowski, Walt↗

DOE OSTI2024

Accelerator Physics at NSLS-II: Research Accomplishments in 2024

NSLS-II accelerator physicists advanced the operational performance and scientific capabilities of NSLS-II, providing regular lattice characterization and correction, injec tion optimization, vertical emittance control, and beam dynamics reports with corre lation analysis. We further developed advanced lattice characterization techniques and studies on impedance, beam-induced heating, and higher-harmonic RF cavity effects to support NSLS-II and its high-brightness upgrade. The assessment of free-electron laser options for the NSLS-II upgrade has been completed. We carried out comprehensive studies focused on complex bend magnets and novel efficient injection schemes for next-generation low-emittance synchrotrons. We contributed to the Electron-Ion Collider project, including Electron Storage Ring lattice design, beam diagnostics, and injector studies. The physicists participated in international collaborations, including the development of Python-based Middle Layer software, and participated in key accel erator physics workshops and scientific meetings. The main research accomplishments achieved in 2024 are summarized in this report.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

LLM Benchmarking with LLaMA2: Evaluating Code Development Performance Across Multiple Programming Languages

The rapid evolution of large language models (LLMs) has opened new possibilities for automating various tasks in software development. This paper evaluates the capabilities of the LLaMA 2-70B model in automating these tasks for scientific applications written in commonly used programming languages. Using representative test problems, we assess the model's capacity to generate code, documentation, and unit tests, as well as its ability to translate existing code between commonly used programming languages. Our comprehensive analysis evaluates the compilation, runtime behavior, and correctness of the generated and translated code. Additionally, we assess the quality of automatically generated code, documentation, and unit tests. Here, our results indicate that while LLaMA 2-70B frequently generates syntactically correct and functional code for simpler numerical tasks, it encounters substantial difficulties with more complex, parallelized, or distributed computations, requiring considerable manual corrections. We identify key limitations and suggest areas for future improvements to better leverage AI-driven automation in scientific computing workflows.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2002

Software Engineering Support of the Third Round of Scientific Grand Challenge Investigations: An Earth Modeling System Software Framework Strawman Design that Integrates Cactus and UCLA/UCB Distributed Data Broker

One of the most significant challenges in large-scale climate modeling, as well as in high-performance computing in other scientific fields, is that of effectively integrating many software models from multiple contributors. A software framework facilitates the integration task. both in the development and runtime stages of the simulation. Effective software frameworks reduce the programming burden for the investigators, freeing them to focus more on the science and less on the parallel communication implementation, while maintaining high performance across numerous supercomputer and workstation architectures. This document proposes a strawman framework design for the climate community based on the integration of Cactus, from the relativistic physics community, and UCLA/UCB Distributed Data Broker (DDB) from the climate community. This design is the result of an extensive survey of climate models and frameworks in the climate community as well as frameworks from many other scientific communities. The design addresses fundamental development and runtime needs using Cactus, a framework with interfaces for FORTRAN and C-based languages, and high-performance model communication needs using DDB. This document also specifically explores object-oriented design issues in the context of climate modeling as well as climate modeling issues in terms of object-oriented design.

Talbot, Bryan↗

NASA NTRS2006

"One-Stop Shopping" for Ocean Remote-Sensing and Model Data

OurOcean Portal 2.0 (http:// ourocean.jpl.nasa.gov) is a software system designed to enable users to easily gain access to ocean observation data, both remote-sensing and in-situ, configure and run an Ocean Model with observation data assimilated on a remote computer, and visualize both the observation data and the model outputs. At present, the observation data and models focus on the California coastal regions and Prince William Sound in Alaska. This system can be used to perform both real-time and retrospective analyses of remote-sensing data and model outputs. OurOcean Portal 2.0 incorporates state-of-the-art information technologies (IT) such as MySQL database, Java Web Server (Apache/Tomcat), Live Access Server (LAS), interactive graphics with Java Applet at the Client site and MatLab/GMT at the server site, and distributed computing. OurOcean currently serves over 20 real-time or historical ocean data products. The data are served in pre-generated plots or their native data format. For some of the datasets, users can choose different plotting parameters and produce customized graphics. OurOcean also serves 3D Ocean Model outputs generated by ROMS (Regional Ocean Model System) using LAS. The Live Access Server (LAS) software, developed by the Pacific Marine Environmental Laboratory (PMEL) of the National Oceanic and Atmospheric Administration (NOAA), is a configurable Web-server program designed to provide flexible access to geo-referenced scientific data. The model output can be views as plots in horizontal slices, depth profiles or time sequences, or can be downloaded as raw data in different data formats, such as NetCDF, ASCII, Binary, etc. The interactive visualization is provided by graphic software, Ferret, also developed by PMEL. In addition, OurOcean allows users with minimal computing resources to configure and run an Ocean Model with data assimilation on a remote computer. Users may select the forcing input, the data to be assimilated, the simulation period, and the output variables and submit the model to run on a backend parallel computer. When the run is complete, the output will be added to the LAS server for

Li, P. Peggy↗

NASA NTRS2004

Developing Software for NASA Missions in the New Millennia

NASA is working on new mission concepts for exploration of the solar system. The concepts for these missions include swarms of hundreds of cooperating intelligent spacecraft which will be able to work in teams and gather more data than current single spacecraft missions. These spacecraft will not only have to operate independently for long periods of time on their own and in teams, but will also need to have autonomic properties of self healing, self configuring, self optimizing and self protecting for them to survive in the harsh space environment. Software for these types of missions has never been developed before and represents some of the challenges of software development in the new millennia. The Autonomous Nano Technology Swarm (ANTS) mission is an example of one of the swarm missions NASA is considering. The ANTS mission will use a swarm of one thousand pico-spacecraft that weigh less than five pounds. Using an insect colony analog, ANTS will explore the asteroid belt and catalog the mass, density, morphology, and chemical composition of the asteroids. Due to the size of the spacecraft, each will only carry a single miniaturized science instrument which will require them to cooperate in searching for asteroids that are of scientific interest. This article also discusses the ANTS mission, the properties the spacecraft will need and how that will effect future software development.

Truszkowski, Walt↗

DOE OSTI2025

A Tale from the Trenches: Applying Metamorphic and Differential Testing to Bioinformatics Software

Metamorphic and differential testing have been proposed as best practices for testing software that is difficult to test, such as for programs in scientific domains. An assumption is that these approaches can be easily customized and applied to almost any domain. However, scientific software is often data-driven, and metamorphic relations may require significant domain knowledge to develop. In addition, tools are often written for ad-hoc experimentation by the scientists and often embed many assumptions about the importance and representation of different natural phenomena. In this paper, we present our experience applying both metamorphic and differential testing to a set of four computational biology tools that predict the growth of an organism. While our original goal was to evaluate these techniques to improve our system-level testing, we encountered multiple roadblocks along the way. Although we did find faults (some confirmed by developers), we also uncovered a set of challenges, including the considerable manual effort required for (a) defining domain-specific tests, (b) validating correctness, and (c) distinguishing between issues stemming from poor data and those arising from incorrect software.

Marsh, Alexis L [Iowa State University/Ames Labora↗

NASA NTRS1984

Materials properties data base computerization

Material property data plays a key role in the design of jet engine components. Consistency, accuracy and efficient use of material property data is of prime importance to the engineering community. The system conception, development, implementation, and future plans for computer software that captures the Material Properties Handbook into a scientific data base are described. The engineering community is given access to raw data and property curves, display of multiple curves for material evaluation and selection, direct access by design analysis computer programs, display of the material specification, and a historical repository for the material evolution. The impact of this activity includes significant productivity gains and cost reductions; all users have access to the same information nd provides consistent, rapid response to the needs of the engineering community. Future plans include incorporating the materials properties data base into a network environment to access information from other data bases and download information to engineering work stations.

Baur, R. G.↗

NASA NTRS1985

FORTH as the basis for an integrated operations environment for a Space Shuttle scientific experiment

Over a period of three years, a FORTH-based system was developed by JPL for the operations of a major scientific instrument onboard the Space Shuttle. The software had to meet a very demanding operations environment where the interactiveness of the software was not merely desirable but essential to the success of the mission. Forth was chosen for its capability of integrating divergent software needs into an interactive package. The mission flown in October 1984 was beset with numerous hardware failures and challenged the capability of the system to its fullest.

Harris, Henry M.↗

NASA NTRS1998

Studying the Earth's Environment from Space: Computer Laboratory Exercised and Instructor Resources

Studying the Earth's Environment From Space is a two-year project to develop a suite of CD-ROMs containing Earth System Science curriculum modules for introductory undergraduate science classes. Lecture notes, slides, and computer laboratory exercises, including actual satellite data and software, are being developed in close collaboration with Carla Evans of NASA GSFC Earth Sciences Directorate Scientific and Educational Endeavors (SEE) project. Smith and Alfultis are responsible for the Oceanography and Sea Ice Processes Modules. The GSFC SEE project is responsible for Ozone and Land Vegetation Modules. This document constitutes a report on the first year of activities of Smith and Alfultis' project.

Smith, Elizabeth A.↗

NASA NTRS1998

Synaptic changes in rat maculae in space and medical imaging: the link

Two different space life sciences missions (SLS-1 and SLS-2) have demonstrated that the synapses of the hair cells of rat vestibular maculae increase significantly in microgravity. The results also indicate that macular synapses are sensitive to stress. These findings argue that vestibular maculae exhibit neuroplasticity to macroenvironmental and microenvironmental changes. This capability should be clinically relevant to rehabilitative training and/or pharmacological treatments for vestibular disease. The results of this ultrastructural research also demonstrated that type I and type II hair cells are integrated into the same neuronal circuitry. The findings were the basis for development of three-dimensional reconstruction software to learn details of macular wiring. This software, produced for scientific research, has now been adapted to reconstruct the face and skull directly from computerized tomography scans. In collaboration with craniofacial reconstructive surgeons at Stanford University Medical Center, an effort is under way to produce a virtual environment workbench for complex craniofacial surgery. When completed, the workbench will help surgeons train for and simulate surgery. The methods are patient specific. This research illustrates the value of basic research in leading to unanticipated medical applications.

Flight Experiment↗

NASA NTRS2010

The Software Correlator of the Chinese VLBI Network

The software correlator of the Chinese VLBI Network (CVN) has played an irreplaceable role in the CVN routine data processing, e.g., in the Chinese lunar exploration project. This correlator will be upgraded to process geodetic and astronomical observation data. In the future, with several new stations joining the network, CVN will carry out crustal movement observations, quick UT1 measurements, astrophysical observations, and deep space exploration activities. For the geodetic or astronomical observations, we need a wide-band 10-station correlator. For spacecraft tracking, a realtime and highly reliable correlator is essential. To meet the scientific and navigation requirements of CVN, two parallel software correlators in the multiprocessor environments are under development. A high speed, 10-station prototype correlator using the mixed Pthreads and MPI (Massage Passing Interface) parallel algorithm on a computer cluster platform is being developed. Another real-time software correlator for spacecraft tracking adopts the thread-parallel technology, and it runs on the SMP (Symmetric Multiple Processor) servers. Both correlators have the characteristic of flexible structure and scalability.

Zheng, Weimin↗

DOE OSTI2024

Introducing NOODLES: Collaborative Visualization in a Flavorful Package

We introduce NOODLES, a lightweight collaborative visualization and analysis protocol. NOODLES was developed to enable new scientific workflows while enhancing existing pipelines. Using a technology-minimal approach to strengthen applicability, this protocol allows researchers to tie disparate software together as well as making domain specific visualizations accessible across various platforms and form factors. In this talk we discuss background, challenges, and gaps in the current tool landscape that lead to the development of the protocol. We then describe the design of the protocol and present several use cases to demonstrate the efficacy of NOODLES in addressing complex visualization challenges and how it co-exists with existing tools. We conclude by outlining in-progress work and potential avenues for future development within the NOODLES framework.

collaborative analysis↗

NASA NTRS2013

Guidance, Navigation, and Control Technology Assessment for Future Planetary Science Missions

Future planetary explorations envisioned by the National Research Council's (NRC's) report titled Vision and Voyages for Planetary Science in the Decade 2013-2022, developed for NASA Science Mission Directorate (SMD) Planetary Science Division (PSD), seek to reach targets of broad scientific interest across the solar system. This goal requires new capabilities such as innovative interplanetary trajectories, precision landing, operation in close proximity to targets, precision pointing, multiple collaborating spacecraft, multiple target tours, and advanced robotic surface exploration. Advancements in Guidance, Navigation, and Control (GN&C) and Mission Design in the areas of software, algorithm development and sensors will be necessary to accomplish these future missions. This paper summarizes the key GN&C and mission design capabilities and technologies needed for future missions pursuing SMD PSD's scientific goals.

position↗

DOE OSTI2023

Good Practices for High-Quality Scientific Computing

Experimental and observational sciences have developed robust practices for conducting experiments, maintaining their instruments, and record keeping for provenance. Computational science has only recently begun to confront the issue of quality of their instrument, the software, and the credibility of their scientific output. Most of the available literature in software engineering relates to enterprise software. While it can inform practices in scientific software, adjustments are usually needed. From time to time quality conscious practitioners have published collections of best practices for scientific software. Here, this article provides one more such list but with updated suggestions, motivated by the need to keep up with the rapid changes in the computing industry.

97 MATHEMATICS AND COMPUTING↗